Hi,

On Friday, January 11, 2013, David Iles wrote:

> Hi Folks,
>
> I want to run a GSVA analysis on a set of Affymetrix hgu133plus2 arrays.
> To familiarise myself with the GSVA code, I worked through the example in
> the vignette, but encountered the following issue...
>
> > data(leukemia)
> > data(c2BroadSets)
> > library(parallel)
> > filtered_eset <- nsFilter(leukemia_eset, require.entrez=TRUE,
> remove.dupEntrez=TRUE,
> +                           var.func=IQR, var.filter=TRUE, var.cutoff=0.5,
> filterByQuantile=TRUE,
> +                           feature.exclude="^AFFX")
> > leukemia_filtered_eset <- filtered_eset$eset
> > leukemia_es <- gsva(leukemia_filtered_eset, c2BroadSets, min.sz=10,
> max.sz=500, verbose=TRUE)$es.obs
> Mapping identifiers between gene sets and feature names
>   |
>                                         |   0%)
>
> The process has forked and you cannot use this CoreFoundation
> functionality safely. You MUST exec().
> Break on
> __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNCTIONALITY___YOU_MUST_EXEC__()
> to debug.
>
> ....etcetcetc. The process hangs here.
>
> I get the same messages with my own data. I must have overlooked
> something. Any suggestions?


You will unfortunately get this from time to time when you are running R
through R.app on a Mac.

I'm not sure if running through Rstudio would sidestep this problem (maybe
yes, so give that a try first if you like to use a GUI).  If that doesn't
work, running through the terminal, or emacs/ESS should do the trick.

HTH,
-Steve


>
> Dr David Iles
> School of Biology
> University of Leeds
> Leeds LS2 9JT
>
> d.e.iles@leeds.ac.uk <javascript:;><mailto:d.e.iles@leeds.ac.uk<javascript:;>
> >
>
> > sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] parallel  grid      stats     graphics  grDevices utils     datasets
>  methods   base
>
> other attached packages:
>  [1] RBGL_1.34.0          BiocInstaller_1.8.3  GSVAdata_0.99.9
>  hgu95a.db_2.8.0      org.Hs.eg.db_2.8.0
>  [6] RSQLite_0.11.2       DBI_0.2-5            GSVA_1.6.1
> GSEABase_1.20.1      annotate_1.36.0
> [11] AnnotationDbi_1.20.3 Rgraphviz_2.2.1      graph_1.36.1
> RColorBrewer_1.0-5   limma_3.14.3
> [16] genefilter_1.40.0    Biobase_2.18.0       BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.16.4  splines_2.15.2  stats4_2.15.2   survival_2.37-2
> tools_2.15.2    XML_3.95-0.1    xtable_1.7-0
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org <javascript:;>
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>


-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

	[[alternative HTML version deleted]]

